Tomato Leaf Curl New Delhi Virus: An Emerging Virus Complex Threatening Vegetable and Fiber Crops
TL;DR: ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus.
Abstract: The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade Special emphasis has been given to gene silencing suppression ability in order to counteract host plant defense responses The importance of the interaction with DNA alphasatellites and betasatellites in the biology of the virus has been demonstrated ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus Recombination and pseudorecombination have been shown as motors of diversification and adaptive evolution Important progress has also been made in control strategies to reduce disease damage This review highlights these various achievements in the context of the previous knowledge of begomoviruses and their interactions with plants
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25 Jan 2021
TL;DR: A review of global virus disease pandemics and major epidemics that originated within different world regions, spread to other continents, and now have very wide distributions can be found in this article.
Abstract: The world's staple food crops, and other food crops that optimize human nutrition, suffer from global virus disease pandemics and epidemics that greatly diminish their yields and/or produce quality. This situation is becoming increasingly serious because of the human population's growing food requirements and increasing difficulties in managing virus diseases effectively arising from global warming. This review provides historical and recent information about virus disease pandemics and major epidemics that originated within different world regions, spread to other continents, and now have very wide distributions. Because they threaten food security, all are cause for considerable concern for humanity. The pandemic disease examples described are six (maize lethal necrosis, rice tungro, sweet potato virus, banana bunchy top, citrus tristeza, plum pox). The major epidemic disease examples described are seven (wheat yellow dwarf, wheat streak mosaic, potato tuber necrotic ringspot, faba bean necrotic yellows, pepino mosaic, tomato brown rugose fruit, and cucumber green mottle mosaic). Most examples involve long-distance virus dispersal, albeit inadvertent, by international trade in seed or planting material. With every example, the factors responsible for its development, geographical distribution and global importance are explained. Finally, an overall explanation is given of how to manage global virus disease pandemics and epidemics effectively.
92 citations
TL;DR: This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops and the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution.
Abstract: Virus disease pandemics and epidemics that occur in the world's staple food crops pose a major threat to global food security, especially in developing countries with tropical or subtropical climates. Moreover, this threat is escalating rapidly due to increasing difficulties in controlling virus diseases as climate change accelerates and the need to feed the burgeoning global population escalates. One of the main causes of these pandemics and epidemics is the introduction to a new continent of food crops domesticated elsewhere, and their subsequent invasion by damaging virus diseases they never encountered before. This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops. This spillover requires new encounters at the managed and natural vegetation interface. The principal virus disease pandemic examples described are two (cassava mosaic, cassava brown streak) that threaten food security in sub-Saharan Africa (SSA), and one (tomato yellow leaf curl) doing so globally. A further example describes a virus disease pandemic threatening a major plantation crop producing a vital food export for West Africa (cacao swollen shoot). Also described are two examples of major virus disease epidemics that threaten SSA's food security (rice yellow mottle, groundnut rosette). In addition, brief accounts are provided of two major maize virus disease epidemics (maize streak in SSA, maize rough dwarf in Mediterranean and Middle Eastern regions), a major rice disease epidemic (rice hoja blanca in the Americas), and damaging tomato tospovirus and begomovirus disease epidemics of tomato that impair food security in different world regions. For each pandemic or major epidemic, the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution, are explained. Finally, clarification is provided over what needs to be done globally to achieve effective management of severe virus disease pandemics and epidemics initiated by spillover events.
41 citations
29 Apr 2020
TL;DR: This is the first report demonstrating that ToLCNDV is a seed-transmissible virus in zucchini squash plants in Italy and Mechanical transmission from seed-borne virus-infected seedlings to healthy zuchetti squash plants was succesful, demonstrating that seedlings from To LCNDV- Infected seeds did act as inoculum.
Abstract: Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus affecting tomato cultivation on the Indian subcontinent. Recently, however, a new strain of the virus, named ToLCNDV-ES, has spread to Mediterranean countries such as Spain, Italy, and Tunisia, and occurred in Cucurbita crops, causing economic damage. Although ToLCNDV is spread by the sweet potato whitefly (Bemisia tabaci), like other begomoviruses, it has not been clear how ToLCNDV suddenly spread from the Indian subcontinent to the Mediterranean region. In 2017, ToLCNDV was diagnosed in young seedlings germinated naturally from fruits fallen in the prior year on a farm located in Giugliano in Campania, Naples, Italy, suggesting a possible role of the seeds in vertical transmission of the virus. Because sweet potato whiteflies were widespread naturally in that region, it was necessary to verify that in an artificial insect vector-free condition. Seeds were harvested from two ToLCNDV-infected zucchini squash cultivars in Naples in 2017 and 2018 to examine whether ToLCNDV can be transmitted from zucchini squash seeds to young plants. Viral DNA was amplified from these seeds and 1- to 3-week-old seedlings germinated from them with a ToLCNDV-specific primer set. According to PCR results, viral contamination was confirmed from all harvested seeds and dissemination was proven from 61.36% of tested seedling samples. Mechanical transmission from seed-borne virus-infected seedlings to healthy zucchini squash plants was also succesful, demonstrating that seedlings from ToLCNDV-infected seeds did act as inoculum. This is the first report demonstrating that ToLCNDV is a seed-transmissible virus in zucchini squash plants in Italy.
31 citations
TL;DR: This research presents the results of a two-year study aimed at determining the phytochemical barriers to sustainable plant growth in Sicily and its environs.
Abstract: S. Panno, A. G. Caruso, E. Troiano, M. Luigi, A. Manglli, T. Vatrano, G. Iacono, S. Marchione, S. Bertin, L. Tomassoli, G. Parrella and S. Davino* Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, bld 5, 90128 Palermo; Angelo and Salvatore Lima Mancuso Foundation, University of Palermo, Piazza Marina, 61, 90133 Palermo; Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), s.s. Portici, Via dell’Universit a 133, 80055 Portici; Research Centre for Plant Protection and Certification (CREA), Via C.G. Bertero 22, Rome; via Einaudi, 9 – 88021 Borgia; Department of Agriculture, Food and Environment (Di3A), University of Catania, Via S. Sofia 100, 95123 Catania; Osservatorio per le Malattie delle Piante di Palermo (OMP), Via Uditore 15, 90145 Palermo; and Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Turin, Italy
28 citations
Cites background or result from "Tomato Leaf Curl New Delhi Virus: A..."
...It has been demonstrated that ToLCNDV-ES is probably the result of genetic recombination between a ToLCNDV-type isolate and other begomoviruses (Moriones et al., 2017)....
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...As reported by different authors (Ju arez et al., 2014; Mnari-Hattab et al., 2015; Luigi et al., 2016; Panno et al., 2016; Moriones et al., 2017), ToLCNDV in the Mediterranean basin found zucchini squash as its elected host....
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...As ToLCNDV rapidly spread in a few years within the Mediterranean area, the low level of variability found among isolates supports the hypothesis of the founder effect associated with a population bottleneck during the spread to this new area (Moriones et al., 2017)....
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...Therefore, these isolates constitute a new strain of this virus, for which the name ES (ToLCNDV-ES) was proposed (Moriones et al., 2017)....
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TL;DR: The role of high-throughput sequencing (HTS) in these discoveries and its general impact on tomato virome research was discussed in this article, where the authors observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS.
Abstract: Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011-2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
27 citations
References
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TL;DR: Results suggest that virus-encoded suppressors of gene silencing have distinct modes of action, are targeted against distinct components of the host gene-silencing machinery, and that there is dynamic evolution of theHost and viral components associated with the gene- silencing mechanism.
Abstract: In transgenic and nontransgenic plants, viruses are both initiators and targets of a defense mechanism that is similar to posttranscriptional gene silencing (PTGS). Recently, it was found that potyviruses and cucumoviruses encode pathogenicity determinants that suppress this defense mechanism. Here, we test diverse virus types for the ability to suppress PTGS. Nicotiana benthamiana exhibiting PTGS of a green fluorescent protein transgene were infected with a range of unrelated viruses and various potato virus X vectors producing viral pathogenicity factors. Upon infection, suppression of PTGS was assessed in planta through reactivation of green fluorescence and confirmed by molecular analysis. These experiments led to the identification of three suppressors of PTGS and showed that suppression of PTGS is widely used as a counter-defense strategy by DNA and RNA viruses. However, the spatial pattern and degree of suppression varied extensively between viruses. At one extreme, there are viruses that suppress in all tissues of all infected leaves, whereas others are able to suppress only in the veins of new emerging leaves. This variation existed even between closely related members of the potexvirus group. Collectively, these results suggest that virus-encoded suppressors of gene silencing have distinct modes of action, are targeted against distinct components of the host gene-silencing machinery, and that there is dynamic evolution of the host and viral components associated with the gene-silencing mechanism.
1,094 citations
"Tomato Leaf Curl New Delhi Virus: A..." refers background in this paper
...Interestingly viral proteins coded by these ORFs have roles in pathogenicity and RSS activity....
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...AV1 codes for coat protein, and AV2 (overlapped to AV1) encodes for a pre coat protein with an additional probable role as RSS [32]....
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...The ORF AC2 encodes for a 15-kDa protein that in begomoviruses also functions as a pathogenicity factor and RSS [30]....
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...To counter host defense, begomoviruses are equipped with proteins with RSS activity that regulate pathogenicity....
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...The ORF AC4 is embedded in the AC1 gene and is characterized as a pathogenicity determinant as well as an RNA-silencing suppressor (RSS) [29]....
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TL;DR: Human activity has also played an important role in the emergence of serious geminivirus diseases across the globe, like the changes in cropping systems, the introduction of new crops, the movement of infected planting materials and the introducing of host susceptibility genes through the exchange of germplasm.
Abstract: Summary
Geminiviruses form the second largest family of plant viruses, the Geminiviridae, represented by four genera: Mastrevirus, Curtovirus, Topocuvirus and Begomovirus. During the last two decades these viruses have emerged as devastating pathogens, particularly in the tropics and subtropics, causing huge economic losses and threatening crop production. Epidemics caused by re-emerging and newly emerging geminiviruses are becoming frequent even in regions that were earlier free from these viruses. Compared to mastreviruses and curtoviruses, begomoviruses have emerged as more serious problems in a variety of crops, for example, cassava, cotton, grain legumes and vegetables. Major contributory factors for the emergence and spread of new geminivirus diseases are the evolution of variants of the viruses, the appearance of the whitefly ‘B’ biotype and the increase in the vector population. Variability in geminiviruses has arisen through mutations, recombination and pseudorecombination. Genomic recombination in geminiviruses, not only between the variants of the same virus but also between species and even between genera, has resulted in rapid diversification. From the disease point of view, most virulent variants have developed through recombination of viral genomes such as those associated with cassava mosaic, cotton leaf curl, and tomato leaf curl diseases. Heterologous recombinants containing parts of the host genome and/or sequences from satellite-like molecules associated with monopartite begomoviruses provide unlimited evolutionary opportunities. Human activity has also played an important role in the emergence of serious geminivirus diseases across the globe, like the changes in cropping systems, the introduction of new crops, the movement of infected planting materials and the introduction of host susceptibility genes through the exchange of germplasm.
693 citations
TL;DR: This Review describes the current knowledge of how geminiviruses interact with their plant hosts and the functional consequences of these interactions.
Abstract: The family Geminiviridae is one of the largest and most important families of plant viruses. The small, single-stranded DNA genomes of geminiviruses encode 5-7 proteins that redirect host machineries and processes to establish a productive infection. These interactions reprogramme plant cell cycle and transcriptional controls, inhibit cell death pathways, interfere with cell signalling and protein turnover, and suppress defence pathways. This Review describes our current knowledge of how geminiviruses interact with their plant hosts and the functional consequences of these interactions.
590 citations
"Tomato Leaf Curl New Delhi Virus: A..." refers background in this paper
...The DNA-B has two ORFs (BC1 and BV1) that encode two proteins involved in the movement of the virus and its gene products [27,28]....
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TL;DR: Revised guidelines for the classification and nomenclature of begomoviruses are proposed and genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomviruses belonging to different species and strains, respectively.
Abstract: Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.
537 citations
"Tomato Leaf Curl New Delhi Virus: A..." refers background or methods in this paper
...Thus, based on DNA-A pairwise nucleotide sequence comparisons and criteria for species/strain demarcation currently accepted by the ICTV for begomoviruses (≥91% and ≥94% nucleotide sequence identity for species and strain demarcation, respectively) [37] it was shown by Fortes et al. [7] that most of the ToLCNDV isolates from the Asian locations were in a single group of closely related DNA-A sequences (≥94% identity) despite the high diversity of host species and geographic origin or...
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...Therefore, according to ICTV guidelines, isolates of at least seven different strains are currently present in the population of ToLCNDV that differ genetically (≤94% nucleotide sequence identity) between them and from isolates that belong to the largely predominant ToLCNDV-type group....
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...Isolates that differed at the strain threshold level according to criteria for species/strain demarcation currently accepted for begomoviruses by the ICTV [37] (marked with asterisks in Supplementary Materials Table S1) are highlighted with colored letters....
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...Phylogenetic relationships among the full-length DNA-A sequences of 136 isolates of ToLCNDV available in the NCBI/GenBank a d I ter ational Committee on Taxonomy of Viruses (ICTV) databases s of 10 July 2017....
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...As for other begomoviruses and according to the guidelines of the International Committee on Taxonomy of Viruses (ICTV), these DNA-A sequences can be used for taxonomic purposes [37]....
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TL;DR: UgV isolates were detected in severely mosaic-affected plants from all 11 widely separated locations sampled, and the probable role of recombination in geminivirus evolution in the short to medium term is discussed.
Abstract: Geminivirus isolates associated with the epidemic of severe cassava mosaic disease in Uganda were studied and compared with virus isolates from the part of Uganda outside the epidemic area, and with African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV). Isolates of a novel type [the Uganda variant (UgV)] were detected in severely affected plants from the epidemic area, whereas those from plants outside the epidemic area were typical of ACMV. The complete nucleotide sequences of DNA-A of UgV (2799 nt) and of a Tanzanian isolate of EACMV (2801 nt) were determined and are extremely similar, except for the coat protein (CP) gene. The CP gene of UgV has three distinct regions: the 5' 219 nt are 99% identical to EACMV (only 79% to ACMV); the following 459 nt are 99% identical to ACMV (75% to EACMV); and the 3' 93 nt are 98% identical to EACMV (76% to ACMV). UgV DNA-A therefore is considered to have arisen by interspecific recombination of EACMV and ACMV. Despite the hybrid nature of their CP, UgV isolates were indistinguishable from ACMV in tests with 20 monoclonal antibodies (MAbs), including seven which reacted with ACMV but not EACMV. The discontinuous epitopes detected by these seven MAbs must involve amino acids which lie in the central part of the CP (residues 74-226) and which differ in ACMV and EACMV. UgV isolates were detected in severely mosaic-affected plants from all 11 widely separated locations sampled. The probable role of recombination in geminivirus evolution in the short to medium term is discussed.
477 citations
"Tomato Leaf Curl New Delhi Virus: A..." refers background in this paper
...Thus, significant changes in host adaptation can be observed in recombinant begomoviruses [57] even resulting in severe epidemics [58], suggesting recombination as a mechanism to evolve and adapt to changing environmental conditions....
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